[gmx-users] fitting problem

[Rohit Farmer]

Hi there,

I am trying to fit a protein to a reference structure using the command
below

trjconv -s run.trp -f run.xtc -o run-fit.xtc -fit progressive

I am using protein for least square and system for output.

This command always worked for me but for this particular protein the side
chains get crooked. I don't know how to explain but they look like flat
structures with random bonds between the atoms.

I tried -pbc mol and whole instead of fit just to get rid of the pbc effect
and don't care about fitting. But it also gave the same result.

Can someone please help.

Thanks

Rohit